[DO NOT MERGE] #4974
gatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
20m 25s
Validate script WDLs using womtools
56s
Validate generated WDLs using womtools
14m 9s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
17 errors and 19 warnings
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_M2_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
Process completed with exit code 1.
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Java 17.0.6+10 build and test cloud
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
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Java 17.0.6+10 build and test unit
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
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Java 17.0.6+10 test on docker variantcalling
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183405-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Worker.JobRunner.RunAsync(AgentJobRequestMessage message, CancellationToken jobRequestCancellationToken)
at GitHub.Runner.Worker.JobRunner.RunAsync(AgentJobRequestMessage message, CancellationToken jobRequestCancellationToken)
at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
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Java 17.0.6+10 test on docker variantcalling
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
|
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Java 17.0.6+10 test on docker unit
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Common.Tracing.Error(Exception exception)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at System.Diagnostics.TraceSource.Flush()
at GitHub.Runner.Common.Tracing.Dispose(Boolean disposing)
at GitHub.Runner.Common.Tracing.Dispose()
at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing)
at GitHub.Runner.Common.TraceManager.Dispose()
at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing)
at GitHub.Runner.Common.HostContext.Dispose()
at GitHub.Runner.Worker.Program.Main(String[] args)
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Java 17.0.6+10 test on docker unit
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
|
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Java 17.0.6+10 test on docker conda
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Common.Tracing.Error(Exception exception)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at System.Diagnostics.TraceSource.Flush()
at GitHub.Runner.Common.Tracing.Dispose(Boolean disposing)
at GitHub.Runner.Common.Tracing.Dispose()
at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing)
at GitHub.Runner.Common.TraceManager.Dispose()
at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing)
at GitHub.Runner.Common.HostContext.Dispose()
at GitHub.Runner.Worker.Program.Main(String[] args)
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Java 17.0.6+10 test on docker conda
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
|
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Java 17.0.6+10 build and test integration
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
|
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Java 17.0.6+10 test on docker integration
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message)
at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
at GitHub.Runner.Common.Tracing.Error(Exception exception)
at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args)
Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20250110-183406-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk)
at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
at System.Diagnostics.TextWriterTraceListener.Flush()
at System.Diagnostics.TraceSource.Flush()
at GitHub.Runner.Common.Tracing.Dispose(Boolean disposing)
at GitHub.Runner.Common.Tracing.Dispose()
at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing)
at GitHub.Runner.Common.TraceManager.Dispose()
at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing)
at GitHub.Runner.Common.HostContext.Dispose()
at GitHub.Runner.Worker.Program.Main(String[] args)
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Java 17.0.6+10 test on docker integration
The hosted runner: GitHub Actions 320 lost communication with the server. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
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Java 17.0.6+10 test on docker integration
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
|
|
check if the environment has privileges
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Validate script WDLs using womtools
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 44 MB
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_M2_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_M2_WDL on cromwell
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 27 MB
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Validate generated WDLs using womtools
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Java 17.0.6+10 build and test cloud
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 build and test unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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build and push gatk docker to artifacts
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Java 17.0.6+10 test on docker variantcalling
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 test on docker unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 test on docker conda
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Java 17.0.6+10 build and test integration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 test on docker integration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 test on docker integration
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 2 MB
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Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
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gatkDockerImage
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4.7 GB |
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test-results-17.0.6+10-cloud
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82 KB |
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test-results-17.0.6+10-integration
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575 KB |
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test-results-17.0.6+10-unit
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5.57 MB |
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